DNA-based Complexes Research Articles

DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications.

Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.

PH-responsive i-motif-conjugated nanoparticles for MRI analysis.

Gadolinium (Gd)-based contrast agents (CAs) are widely used to enhance anatomical details in magnetic resonance imaging (MRI). Significant research has expanded the field of CAs into bioresponsive CAs by modulating the signal to image and monitor biochemical processes, such as pH. In this work, we introduce the modular, dynamic actuation mechanism of DNA-based nanostructures as a new way to modulate the MRI signal based on the rotational correlation time, τR. We combined a pH-responsive oligonucleotide (i-motif) and a clinical standard CA (Gd-DOTA) to develop a pH-responsive MRI CA. The i-motif folds into a quadruplex under acidic conditions and was incorporated onto gold nanoparticles (iM-GNP) to achieve increased relaxivity, r1, compared to the unbound i-motif. In vitro, iM-GNP resulted in a significant increase in r1 over a decreasing pH range (7.5-4.5) with a calculated pKa = 5.88 ± 0.01 and a 16.7% change per 0.1 pH unit. In comparison, a control CA with a non-responsive DNA strand (T33-GNP) did not show a significant change in r1 over the same pH range. The iM-GNP was further evaluated in 20% human serum and demonstrated a 28.14 ± 11.2% increase in signal from neutral pH to acidic pH. This approach paves a path for novel programmable, dynamic DNA-based complexes for τR-modulated bioresponsive MRI CAs.

Stability of polymeric cationic niosomes and their plasmid DNA-based complexes as gene delivery carriers

This study aims to explore the stability of lipo-polymeric niosomes/niosome-based pCMS-EGFP complexes under different storage temperatures (25 °C, 4 °C, and −20 °C). To date, the question of nucleic acid-complex stability is one of the most vital issues in gene delivery applications. The need for stable vaccines during the COVID-19 pandemic has merely highlighted it. In the case of niosomes as gene carriers, the scientific literature still lacks comprehensive stability studies. In this study, the physicochemical features of niosomes/nioplexes in terms of size, surface charge, and polydispersity index (PDI), along with transfection efficiency, and cytotoxicity in NT2 cells were evaluated for 8 weeks. Compared to day 0, the physicochemical features of the niosomes stored at 25 °C and −20 °C changed dramatically in terms of size, zeta potential, and PDI, while remaining in reasonable values when stored at 4 °C. However, niosomes and nioplexes stored at 4 °C and −20 °C showed nearly stable transfection efficiency values, yet an obvious decrease at 25 °C. This article provides a proof of concept into the stability of polymeric cationic niosomes and their nioplexes as promising gene delivery vehicles. Moreover, it highlights the practical possibility of storing nioplexes at 4 °C for up to 2 months, as an alternative to niosomes, for gene delivery purposes.

Topological gelation of reconnecting polymers

DNA recombination is a ubiquitous process that ensures genetic diversity. Contrary to textbook pictures, DNA recombination, as well as generic DNA translocations, occurs in a confined and highly entangled environment. Inspired by this observation, here, we investigate a solution of semiflexible polymer rings undergoing generic cutting and reconnection operations under spherical confinement. Our setup may be realized using engineered DNA in the presence of recombinase proteins or by considering micelle-like components able to form living (or reversibly breakable) polymer rings. We find that in such systems, there is a topological gelation transition, which can be triggered by increasing either the stiffness or the concentration of the rings. Flexible or dilute polymers break into an ensemble of short, unlinked, and segregated rings, whereas sufficiently stiff or dense polymers self-assemble into a network of long, linked, and mixed loops, many of which are knotted. We predict that the two phases should behave qualitatively differently in elution experiments monitoring the escape dynamics from a permeabilized container. Besides shedding some light on the biophysics and topology of genomes undergoing DNA reconnection in vivo, our findings could be leveraged in vitro to design polymeric complex fluids-e.g., DNA-based complex fluids or living polymer networks-with desired topologies.

Topological digestion drives time-varying rheology of entangled DNA fluids

Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this feat, here we engineer and study DNA-based complex fluids that undergo enzymatically-driven topological and architectural alterations via restriction endonuclease (RE) reactions. We show that these systems display time-dependent rheological properties that depend on the concentrations and properties of the comprising DNA and REs. Through time-resolved microrheology experiments and Brownian Dynamics simulations, we show that conversion of supercoiled to linear DNA topology leads to a monotonic increase in viscosity. On the other hand, the viscosity of entangled linear DNA undergoing fragmentation displays a universal decrease that we rationalise using living polymer theory. Finally, to showcase the tunability of these behaviours, we design a DNA fluid that exhibits a time-dependent increase, followed by a temporally-gated decrease, of its viscosity. Our results present a class of polymeric fluids that leverage naturally occurring enzymes to drive diverse time-varying rheology by performing architectural alterations to the constituents.

Chemical and physical characteristics of hydroxyl group-modified multi-walled carbon nanotube-combined DNA layers

In order to enhance the applicability and functionality of DNA-based complexes, we introduced hydroxyl (–OH) group-modified multi-walled carbon nanotubes (MWCNT–OH), which can aid the dispersion and adsorption in the DNA template. Herein, we fabricated MWCNT–OH-combined DNA and cetyltrimethyl-ammonium chloride-modified DNA (DNA-CTMA) layers using the solution-processed method. The distinct chemical and physical characteristics of the MWCNT–OH-combined DNA and DNA-CTMA layers were examined through various characterisation techniques. For instance, the elemental and surface characteristics were analysed by energy-dispersive x-ray spectroscopy, field emission scanning electron microscopy, and atomic force microscopy. The charge transfer was examined by x-ray photoelectron spectroscopy. In the x-ray photoelectron spectra, a negative peak shift was observed, indirectly indicating that the charge transfer from MWCNT‒OH to DNA occurred. The vibrational and rotational modes were analysed by Raman spectroscopy, and the characteristic functional group and molecular interaction were examined using Fourier transform infrared spectroscopy. As expected, we observed four major characteristic Raman bands of MWCNT–OH in the DNA and DNA-CTMA layers which corresponded to the D-, G-, and G′-bands as well as the strain-induced band. Finally, the light absorption, photoluminescence, and electrical characteristics were examined using UV–vis–NIR spectroscopy, a photoluminescence mapper, and a probe station, respectively. The absorption in the full spectral range, photoluminescence quenching, and current enhancement of DNA and DNA-CTMA layers combined with MWCNT–OH were influenced by the electrostatic and van der Waals interactions between MWCNT–OH and DNA (DNA-CTMA). Our results will provide a simple protocol for constructing composite layers made of organic and inorganic materials which show novel characteristics with easy controllability.

Nonlinear optical behavior of DNA-functionalized gold nanoparticles

The third-order nonlinear optical properties of gold nanoparticles embedded in the DNA-based composites were investigated by means of the third harmonic generation. With this purpose, the thin films comprising DNA-based complexes and Au nanoparticles were spin-deposited on glass substrate and their optical and nonlinear optical features were studied using the Maker-fringe technique at a laser fundamental wavelength of 1064 nm. The values of the third-order susceptibility χ(3)(− 3ω; ω, ω, ω) of the composite films based on DNA complex doped with 5 wt% of N-ethyl-N-(2-hydroxyethyl)-4-(4-nitrophenylazo)aniline were found to be significantly higher than those for pure composite films. Meanwhile, the presence of Au nanoparticles noticeable decreases the third-order nonlinear response of DNA-based composite mainly due to the enhanced absorption and scattering of laser and generated beam, respectively.

Use of Differential Scanning Calorimetry (DSC) to Study the Thermodynamics of DNA-Based Interactions and Nucleic Acid-Based Therapeutics

In the 1950’s, the research findings of James Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins led to the discovery of the deoxyribonucleic acid (DNA) double-helix conformation [1,2]. With DNA at their core, many nucleic acid based assays are used in pharmaceutical, biochemistry, biotechnology, molecular biology, target-based drug design, and other DNA-based technologies [3-7]. In addition, DNA is the molecular target of numerous anti-tumor drugs, anti-viral drugs, and several anti-bacterial agents [8-10]. Historically there have been several approaches in developing some pharmacological and therapeutic agents that interfere with DNA synthesis [8,11]. Since the therapeutic effects of many DNA-binding interactions correlate with thermodynamic profiles of the resulting complexes, elucidation of thermodynamic parameters of such interactions are important in nucleic acid-based therapeutics [12,13]. Differential Scanning Calorimetry (DSC), which provides unique complementary information for nucleic acids, modified nucleic acids, and nucleic acid-ligand interactions, is a powerful method in obtaining thermodynamic parameters. DSC is a direct, model-independent measurement tool that complements, structural and bonding information obtained by various physicochemical methods [13-15]. This review is designed to give the reader a greater understanding of the applications of DSC in DNA-based therapeutics. While this review focuses on calorimetry studies of DNA-based complexes, DSC applications in RNAs have been reviewed elsewhere [16-18].

Sequential programmable self-assembly: Role of cooperative interactions.

We propose a general strategy of "sequential programmable self-assembly" that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenient platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call "DNA spider," that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a "GEOMAG" magnetic construction toy, out of nanoparticles. According to our results, once the binding cooperativity is strong enough, the sequential self-assembly becomes essentially error-free.

Allylic Amination by a DNA–Diene–Iridium(I) Hybrid Catalyst

DNA hybrid catalysis goes organometallic: A DNA strand functionalized with diene ligands forms iridium(I) complexes that can efficiently catalyze an allylic amination in aqueous medium (see scheme). The DNA-based complexes show high stability and activity, and their secondary structure influences the stereoselectivity of the reaction.

NLO properties of functionalized DNA thin films

In this paper we investigate the third-order nonlinear optical properties of spin deposited thin films of DNA-based complexes using the optical third harmonic generation (THG) technique at a fundamental wavelength of 1064 nm. We found that the third-order susceptibility, χ (3)( − 3 ω; ω, ω, ω), of DNA-based films was about one order of magnitude larger than that of our reference, a pure silica slab. In thin films doped with 5% of the chromophore disperse red 1 (DR1), a two order of magnitude larger value of χ (3)( − 3 ω; ω, ω, ω) was observed.

ORGANIZED SUPERSTRUCTURES AT NANOSCALE AND NEW FUNCTIONAL NANOMATERIALS

We report on a number of new effects of self-organization at nanoscale, leading to creation of new functional nanomaterials, including carbon and carbon–metal nanotoroids and nanodiscs and self-assembling of magnetic nanoparticles into helices and chains. We also extensively used a new approach of biopattern nanoengineering to create DNA-based complexes with metal or CdSe / ZnS core-shell nanorods (22 × 4.5 nm) which possess strong linearly polarized photoluminescence due to unidirectional orientation of nanorods along DNA filaments. Optical, electrical, and topological (geometrical) properties of such complexes were investigated. This work is a result of a coherent effort (since 1980s) of a consortium of Russian research groups in Nano-technology (INTC: Interdisciplinary Nanotechnology Consortium) aimed at creating molecular electronic devices based on individual and collective properties of specially designed and fabricated nanoclusters.

Survival of lactic acid bacteria in simulated gastrointestinal juice protected by a DNA-based complex gel

Salmon milt DNA was utilized in the approach to protect functional materials, proteins, microorganisms, drugs, etc., by forming a DNA-based complex gel with gelatin and κ-carrageenan. The multiplier effect of the combination of DNA, gelatin and κ-carrageenan was examined by measuring the release of methyl orange from the gel after being incubated in simulated gastric juice. The results indicated that the hydrogel made of DNA, gelatin and κ-carrageenan can efficiently maintain the functional materials. Furthermore, a complex gel was developed and optimized by applying an emulsion of lactic acid bacteria and cacao oil onto the already prepared hydrogel. The existence of the lactic acid bacteria in the oil emulsion particles was confirmed by scanning electron microscopy. The protection capabilities in the simulated gastrointestinal juice, which had a viability of 1.50 × 106 CFU/g gel after 2 h incubation in the simulated gastric juice and 2.53 × 107 CFU/g gel after 6 h continued incubation in the simulated intestinal juice, were measured, in contrast to 2.58 × 107 CPU/g in the original gel before treatment.